Exchange 2010 - missing mails moved by rules / strange problem

Hello,

one of our users has a pretty strange problem.
First of all, he has 12 rules (11 server-sided plus default for removing categories) and a HUGE folder-tree for about 1.5 years.
His tree looks like:

Inbox
-A
--1
--2
---a
---b
--3 Newsletter
--4
-B
--1
--2
--3 Newsletter
--4
...and so on for 192 folders
Other Stuff
-A
--1
--2
... and so on for 80 folders

Since this week, he complains about missing mails.

While investigating this problem, everything looks fine at first. Mails are stored to his mailbox successfully.

Later we found out, that he has rules to move incoming mails to his "--3 Newsletter" folders depending on sender (and no further processing) and was looking for exactly those mails.
But the mails were not visible in the target folder and neither in the inbox folder.
Using the search function on inbox, I was not able to find the mails. After checking the box for all subfolders, the mail was found. Hovering the mail I was told, that it is in the target folder - where for sure it wasn't.
Opening the mail from the search result and clicking on [File], "Inbox" was displayed as the current folder.

After re-running the matching rule, the mails were visible in the target folder. This worked for yesterday. New mails were moved successfully.
And today, we have the very same problem again. And again, I can quick-fix it by re-running the rules.

As I can see and "fix" this on his machine and on my admin machine, this can't be any local problem.

Any hints or solutions for that?
Our Exchange version 14.3.123.4

(Gosh, this input field is a huge pain in the ass! Why the hell does it automatically uppercase some words?)